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Spectroscopic, reactivity analysis and docking studies of 3-(adamantan-1-yl)-4-(4-fluorophenyl)-1-[(4-phenylpiperazin-1-yl)methyl]-4,5-dihdyro-1H-1,2,4-triazole—5-thione: DFT and MD simulations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Al-Otaibi JS, Mary YS, Mary YS. Spectroscopic analyses on an azatricycloderivative by DFT with different solvents, reactivity analysis and MD simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Al-Mutairi AA, Mary YS, Mary YS, Soman S, Hassan HM, Al-Alshaikh MA, El-Emam AA. Spectroscopic, Docking and MD Simulation Analysis of an Adamantane Derivative with Solvation Effects in Different Solvents. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2086274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Aamal A. Al-Mutairi
- Department of Chemistry, College of Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | | | | | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, Hariyana, India
| | - Hanan M. Hassan
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa City, Egypt
| | - Monirah A. Al-Alshaikh
- Department of Chemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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Al-Otaibi JS, Mary YS, Mary S, Trivedi R, Chakraborty B, Yadav R, Celik I, Soman S. DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2. J Biomol Struct Dyn 2022:1-12. [PMID: 35470781 DOI: 10.1080/07391102.2022.2068649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Ravi Trivedi
- Department of Physics, Indian Institute of Technology, Mumbai, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, Hariyana, India
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Investigation of reactive properties of an antiviral azatricyclo derivative–KDFT, MD and docking simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Hosna S, Janzen DE, Mary YS, Resmi KS, Thomas R, Mohamed R, Wajda S. Molecular structure, spectroscopic, dielectric and thermal study, nonlinear optical properties, natural bond orbital, HOMO-LUMO and molecular docking analysis of (C 6Cl 2O 4) (C 10H 14N 2F) 2·2H 2O. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:328-339. [PMID: 29957411 DOI: 10.1016/j.saa.2018.06.062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/22/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
A new chloranilate compound with 1-(2-fluorophenyl)piperazine has been synthesized and characterized using spectroscopic methods and X-ray diffraction. The atomic arrangement can be described by an H-bonded 3D network, formed by anionic entities, organic cations and H2O molecules linked together via NH…O, OH…Cl, CH…Cl and CH…O hydrogen bonds. The vibrational absorption bands of the various characteristic groups of this compound have been identified by infrared spectroscopy. Moreover, the thermal and dielectric analyses have shown that the title compound has a phase transition at 393 K. The surface mapped over the dnorm property, highlights the A⋯H (AO, C, Cl and F) as the main intermolecular contacts. On the other hand, the geometry, intermolecular bonds and harmonic vibrational frequencies of the title molecule have been investigated using the B3LYP/6-31G (d, p) method. The stability of the structure obtained, as well as the charge transfer within the molecule, have been confirmed by determining the energies of the HOMO and LUMO levels and the theoretical gap energy. Molecular docking studies of the title compound have also been conducted as part of this study.
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Affiliation(s)
- Saadouni Hosna
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia
| | - Daron E Janzen
- Department of Chemistry and Biochemistry, St Catherine University, St Paul, MN, USA
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - K S Resmi
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
| | - Rzaigui Mohamed
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia
| | - Smirani Wajda
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia.
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Zhao P, Li X, Baryshnikov G, Wu B, Ågren H, Zhang J, Zhu L. One-step solvothermal synthesis of high-emissive amphiphilic carbon dots via rigidity derivation. Chem Sci 2018; 9:1323-1329. [PMID: 29675179 PMCID: PMC5887100 DOI: 10.1039/c7sc04607c] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/12/2017] [Indexed: 12/25/2022] Open
Abstract
In nanoscience, amphiphilic carbon dots (ACDs) are of great importance due to their excellent transferability for application in biological sensing, imaging and labelling. However, facile synthetic strategies are still limited, especially for obtaining high-emissive ACDs. Since the development of a high-emissive feature is strongly desired for improving the practical resolution in vivo, here we report a chemical strategy that uses rigid molecules to straightforwardly construct amphiphilic carbon dots (ACDs) with high luminescence quantum yields (QYs). By using 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate (HATU), a typical coplanar compound, as the only precursor, well-defined ACDs were prepared via a one-step solvothermal process which exhibited a superior QY of up to 29%, largely superior to those prepared from precursors with less rigid structures. The effect can be mainly attributed to a significant suppression of the competition of non-radiative decay through rigidity derivation. Metal ionic doping during the synthesis resulted in a further improvement of the crystallinity and monodispersity of the materials, with retention of the high-emissive ability. This high-emissive photoluminescence behavior of the ACDs is accompanied with an excitation-wavelength dependence, a high biocompatibility and a low toxicity, which together make the ACDs advantageous for application in multi-channel bioimaging.
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Affiliation(s)
- Pei Zhao
- State Key Laboratory of Molecular Engineering of Polymers , Department of Macromolecular Science , Fudan University , Shanghai 200433 , China .
| | - Xuping Li
- State Key Laboratory of Molecular Engineering of Polymers , Department of Macromolecular Science , Fudan University , Shanghai 200433 , China .
| | - Glib Baryshnikov
- Division of Theoretical Chemistry , Biology School of Biotechnology , KTH Royal Institute of Technology , SE-10691 Stockholm , Sweden
- Department of Chemistry and Nanomaterials Science , Bogdan Khmelnitsky National University , Cherkasy , 18031 , Ukraine
| | - Bin Wu
- State Key Laboratory of Molecular Engineering of Polymers , Department of Macromolecular Science , Fudan University , Shanghai 200433 , China .
| | - Hans Ågren
- Division of Theoretical Chemistry , Biology School of Biotechnology , KTH Royal Institute of Technology , SE-10691 Stockholm , Sweden
- Institute of Nanotechnology , Spectroscopy and Quantum Chemistry , Siberian Federal University , 660041 Krasnoyarsk , Russia
| | - Junji Zhang
- Key Laboratory for Advanced Materials , Institute of Fine Chemicals , East China University of Science and Technology , Shanghai 200237 , China
| | - Liangliang Zhu
- State Key Laboratory of Molecular Engineering of Polymers , Department of Macromolecular Science , Fudan University , Shanghai 200433 , China .
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